Slows down loading web pages (I know it sounds like a contradiction because on "Advantage" page I wrote "Fast, even with slow connection"). I think it all depends how it is coded and how "heavy" flash implementation is.
Too difficult to use by younger students (K-8) because of the learning curve.
Complex (high learning curve)
Time Consuming to learn
Expensive (program is really targeting professional audience)
When creating a simple action requires good understanding of the program.
Disdvantages